2YPD

Crystal structure of the Jumonji domain of human Jumonji domain containing 1C protein

Structural Biology Knowledgebase: 2YPD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.215

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YPD

Classification: OXIDOREDUCTASE

Total Structure Weight: 94639.28

Macromolecule Entities
Molecule Chains Length Organism Details
PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN 2C A, B 392 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: JUMONJI DOMAIN, RESIDUES 2157-2540
Gene Name(s): JMJD1C Gene View JHDM2C KIAA1380 TRIP8

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EMT
Query on EMT

A, B 2-(ETHYLMERCURI-THIO)-BENZOIC ACID
C9 H10 Hg O2 S
HXQVQGWHFRNKMS-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.215
  • Space Group: P 2 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 45.72 α = 90.00
b = 112.21 β = 90.00
c = 165.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-30
  • Released Date: 2012-12-12
  • Deposition author(s): Vollmar, M., Johansson, C., Krojer, T., Berridge, G., Burgess-Brown, N., Strain-Damerell, C., Froese, S., Williams, E., Goubin, S., Coutandin, D., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

Revision History

  • 2014-09-17
    Type: Source and taxonomy | Details: SOURCE
  • 2014-09-17
    Type: Binding sites and description | Details: REMARK 800, SITE
  • 2014-09-17
    Type: Linkage | Details: LINK
  • 2014-09-17
    Type: Other | Details: REMARK 525, REMARK 610
  • 2014-09-17
    Type: Atom nomenclature | Details: HETATM
  • 2014-09-17
    Type: Non-polymer description | Details: HET, REMARK 620, FORMUL, HETNAM